WHY BY THICKNESS?
There are two ways to cook sous vide, one is based on the thickness of the food and the other is based on the desired tenderness.

Cooking based on thickness is how PolyScience, Baldwin, and Nathan started out as they did research on food safety. Cooking sous vide based on thickness basically tells you the minimum time you can cook a piece of meat to ensure it is safe and comes up to temperature in the middle. It doesn't take into account tenderizing time or any other factors. It's often used by restaurants or home cooks who want to minimize cooking time and are using tender cuts of meat that don't need the tenderization.

Cooking sous vide based on tenderness takes into account how tough a piece of meat is and how long it needs to be cooked in order to make it appealing. So a chuck steak needs to be cooked a lot longer than a filet, even though they are both safe after the same amount of time. As long as the minimum cooking time is met for the temperature used, then it's completely safe to eat.

Both sous vide methods have their uses. Thickness-based is great for very tender cuts cooked by people who need them done in the minimum amount of time. Tenderness-based is best for tougher cuts or people that have a range of time that they are interested in.

NOTES ON THE TIMES
Times were extrapolated from the descriptions in Baldwin's Practical Guide to Sous Vide and Book, as well as Nathan's tables on eGullet and a few other sources.

The times are also approximate since there are many factors that go into how quickly food is heated. The density of the food matters a lot, which is one reason beef heats differently than chicken. To a lesser degree where you get your beef from will also affect the cooking time, and whether the beef was factory raised, farm raised, or grass-fed. Because of this, I normally don't try to pull it out at the exact minute it is done unless I'm in a real rush.

The times shown are also minimum cooking times and food can be, and sometimes needs to be, left in for longer periods in order to fully tenderize the meat. If you are cooking food longer, remember that food should not be cooked at temperatures less than 55ºC (131ºF) for more than 4 hours.